X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 293.0
Details 0.1 M MMT, 30% PEG 1500, +xylitol, K/Na tartrate, 2,6-pyridinecarboxylic acid, 2,4-pyridinecarboxylic acid, 2,5-pyridinecarboxylic acid, 4-pyridazine carboxylic acid, 3-sulfobenzoic acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.25 α = 90
b = 179.18 β = 90
c = 45.22 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-11-12
Diffraction Radiation
Monochromator Protocol
C (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.95 50 99.9 0.094 0.094 -- 9.6 55593 55593 0.0 -3.0 28.6
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.95 1.98 100.0 0.633 0.633 3.0 9.0 2712

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 1.95 50.0 0.0 0.0 52607 52607 2816 99.69 0.1946 0.1946 0.19337 0.21658 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.952 2.002 -- 191 3515 0.26 0.281 -- 99.28
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.366
Anisotropic B[1][1] -0.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.6
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.008
r_gen_planes_refined 0.01
r_chiral_restr 0.104
r_dihedral_angle_4_deg 14.983
r_dihedral_angle_3_deg 12.056
r_dihedral_angle_2_deg 28.923
r_dihedral_angle_1_deg 6.543
r_angle_other_deg 2.395
r_angle_refined_deg 1.707
r_bond_other_d 0.006
r_bond_refined_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5642
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 342

Software

Computing
Computing Package Purpose
MD2 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
HKL-3000:SHELXC/D/E, MLPHARE, DM, ARP/wARP, SOLVE, RESOLVE, CCP4 Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
CCP4 model building
RESOLVE model building
SOLVE model building
ARP/wARP model building
DM model building
MLPHARE model building
HKL-3000:SHELXC/D/E model building
MD2 data collection